ppGaNTase-T6

ABSTRACT

ppGaNTase-T6 polypeptides and polynucleotides and methods for producing such polypeptides by recombinant techniques are disclosed. Also disclosed are methods for utilizing ppGaNTase-T6 polypeptides and polynucleotides in diagnostic assays.

FIELD OF THE INVENTION

[0001] This invention relates to newly identified polypeptides andpolynucleotides encoding such polypeptides, to their use in diagnosisand in identifying compounds that may be agonists, antagonists that arepotentially useful in therapy, and to production of such polypeptidesand polynucleotides.

BACKGROUND OF THE INVENTION

[0002] The drug discovery process is currently undergoing a fundamentalrevolution as it embraces “functional genomics”, that is, highthroughput genome- or gene-based biology. This approach as a means toidentify genes and gene products as therapeutic targets is rapidlysuperceding earlier approaches based on “positional cloning”. Aphenotype, that is a biological function or genetic disease, would beidentified and this would then be tracked back is to the responsiblegene, based on its genetic map position.

[0003] Functional genomics relies heavily on high-throughput DNAsequencing technologies and the various tools of bioinformatics toidentify gene sequences of potential interest from the many molecularbiology databases now available. There is a continuing need to identifyand characterize further genes and their related polypeptides/proteins,as targets for drug discovery.

[0004] Mammalian connective tissues contain proteins, glycoproteins andlarge complex glycoconjugates, such as proteoglycans. Control of thesynthesis, post-translational modification, organization and degradationof these components appears very important in maintaining tissuehomeostasis. Uncontrolled matrix deposition or degradation results inloss of tissue function in virtually all known pathology.

[0005] Articular cartilage is a matrix-rich, avascular, aneural tissuethat allows the fluid articulation of synovial joints. Chondrocytes arethe only cells within this tissue and are responsible for cartilagematrix biosynthesis and assembly and also play a role in matrixcatabolism in diseases, such as osteoarthritis (OA) and rheumatoidarthritis (RA). Cartilage matrix is rich in carbohydrate-containingproteoglycans as well as glycoproteins. In both OA and RA, there appearsto be changes in the synthesis and degradation of the protein cores aswell as changes in the glycosylation patterns of these molecules.

[0006] One of the major articular cartilage matrix components is thelarge proteoglycan, aggrecan. Aggrecan is a glycosoaminoglycan(GAG)-rich molecule that contains chondroitin sulfate and keratansulfate chains as well as N-(asparagine) and O-(serine and threonine)linked oligosaccahrides. The tissue also contains several glycoproteins,some of which are also O-glycosylated.

[0007] Chondroitin sulfate is the predominant GAG on aggrecan. It is arepeating polymer of N-acetylgalactosamine and glucuronic acid. Thesechondroitin sulfate chains are variably sulfated onN-acetylgalactosamine residues in either the 4, 6 or disulfated in boththe 4 and 6 positions. In OA, the length of the chondroitin sulfatechains are shorter and the sulfation pattern changes with an increase in4-sulfation and a reduction in the terminal N-acetylgalactosamine4,6-disulfation (Plass et al. J. Biol. Chem. 273:12642-12649, 1998).These structural changes in the molecule could result in a matrix withlower water binding capacity and may influence interactions with othermatrix components, ultimately resulting in a destabilized matrix.

[0008] Keratan sulfate is the other major GAG on aggrecan and iscovalently attached to the core protein through either an N- orO-linkage (Hascall and Midura in Keratan sulfate chemistry, biology,chemical pathology 1989 eds. H. Greiling and J. Scott, London: TheBiochemical Society, pps 66-75). Serine or threonine post-translationalglycosylation to form keratan sulfate is initiated by transfer ofN-acetylgalactosamine by specific enzymes. The O-linked keratan sulfatepattern changes in the intraglobular domain of aggrecan with aging(Barry et al., J. Biol. Chem. 270:20516-20524, 1995). One of thesevariable glycosylation sites is prone to cleavage by thechondrocyte-derived proteinase, aggrecanase (Arner et al, J. Biol. Chem.274:6594-6601, 1999). Aggrecanase-cleaved aggrecan fragments accumulateat sites of articular cartilage damage in OA and RA (Lark et al., J.Clin. Invest. 100:93-96, 1997) and cleavage activity could be influencedby the glycosylation state of the aggrecan substrate in thisintraglobular domain region. Furthermore, keratan sulfate levels appearto be modulated in patients with OA and has been proposed as a potentialmarker to monitor cartilage matrix turnover (Lohmander, Baillere's Clin.Rhem. 11:711-726, 1997). Changes in the circulating and joint fluidlevels of keratan sulfate could reflect changes in the pattern or levelsof enzymes that are responsible for transferring sugar moieties ontoprotein core. In addition to keratan sulfate, aggrecan contains O-linkedoligosaccharides which may influence its ability to interact with othercomponents to maintain a stable extracellular matrix. Careful analysisof O-linked oligosaccharide changes in aggrecan as cartilage destructionprogresses has not been done; however, it is possible that theseoligosaccharide patterns could also have profound effects on cartilagematrix structure.

[0009] Several UDP-GalNac:polypeptide N-acetylgalactosaminyltransferases(ppGaNTase, EC 2.4.1.41) regulate the initiation of mucin-type 0-linkedglycosylation where N-acetylgalactosamine is transferred to the hydroxylgroup of serine and threonine residues (Clausen and Bennet, Glycobiology6:635-546, 1996). To date, five members of this family (ppGaNTase-T1,-T2, -T3, -T4 and -T5) have been reported in mammalian cells (Clausenand Bennet, Glycobiology 6:635-546, 1996, Bennet et al. J. Biol. Chem.273:30472-30481, 1998, Ten Hagen et al. J. Biol. Chem. 273:27749-27754,1998). Five additional members have been reported in Caenorabditiselegans (Hagen and Nehrke, J. Biol. Chem. 273: 8268-8277, 1998). Presentdata based on some of the characterized enzymes suggest that there aredifferences in substrate specificity as well as the expression patternof these enzymes (Clausen and Bennet, Glycobiology 6:635-546, 1996).Conservation from worms to humans underscores the functional importanceand diversity of this family of enzymes. Families of enzymes responsiblefor carbohydrate addition in glycosaminoglycan synthesis andglycoprotein post-translational modification have been described, andnew members of these families continue to emerge. A new member of theUDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase family ofenzymes termed ppGaNTase-T6 is described herein.

SUMMARY OF THE INVENTION

[0010] The present invention relates to ppGaNTase-T6, in particularppGaNTase-T6 polypeptides and ppGaNTase-T6 polynucleotides, recombinantmaterials and methods for their production. Such polypeptides andpolynucleotides are of interest in relation to methods of treatment ofcertain diseases, including, but not limited to, chronic and acuteinflammation, rheumatoid arthritis, osteoarthritis, septicemia,autoimmune diseases (e.g., inflammatory bowel disease, psoriasis),transplant rejection, graft vs. host disease, infection, stroke,ischemia, acute respiratory disease syndrome, allergy, asthma, renaldisorders, restenosis, fibrosis, brain injury, AIDS, metabolic and otherbone diseases (e.g., osteoporosis), cancer (e.g., lymphoproliferativedisorders), atherosclerosis, and Alzheimers disease, hereinafterreferred to as “diseases of the invention.” In a further aspect, theinvention relates to methods for identifying agonists and antagonists(e.g., inhibitors) using the materials provided by the invention, andtreating conditions associated with ppGaNTase-T6 imbalance with theidentified compounds. In a still further aspect, the invention relatesto diagnostic assays for detecting diseases associated withinappropriate ppGaNTase-T6 activity or levels.

DESCRIPTION OF THE INVENTION

[0011] In a first aspect, the present invention relates to ppGaNTase-T6polypeptides. Such polypeptides include:

[0012] (a) an isolated polypeptide encoded by a polynucleotidecomprising the sequence of SEQ ID NO:1;

[0013] (b) an isolated polypeptide comprising a polypeptide sequencehaving at least 95%, 96%, 97%, 98%, or 99% identity to the polypeptidesequence of SEQ ID NO:2;

[0014] (c) an isolated polypeptide comprising the polypeptide sequenceof SEQ ID NO:2;

[0015] (d) an isolated polypeptide having at least 95%, 96%, 97%, 98%,or 99% identity to the polypeptide sequence of SEQ ID NO:2;

[0016] (e) the polypeptide sequence of SEQ ID NO:2; and

[0017] (f) an isolated polypeptide having or comprising a polypeptidesequence that has an Identity Index of 0.95, 0.96, 0.97, 0.98, or 0.99compared to the polypeptide sequence of SEQ ID NO:2;

[0018] (g) fragments and variants of such polypeptides in (a) to (f).

[0019] Polypeptides of the present invention are believed to be membersof the UDP-GalNac:polypeptide N-acetylgalactosaminyltransferase familyof polypeptides. They are therefore of interest because O-linked sugarsmay help protect glycoproteins from proteolytic processing or add chargeto the molecules to influence their ability to bind other matrixcomponents. It is possible that the post-translational modification ofglycoproteins and GAGs may be controlled by enzymes responsible forglycosylation of the protein core. Interestingly, bone sialoproteinlevels have also been shown to change in patients with destructive jointdisease (Lohmander, Baillere's, Clin. Rhem. 11:711-726, 1997). Together,these studies indicate that glycosylation of cartilage matrix componentscould be key to control appropriate matrix integrity. Theseglycosylation patterns, controlled by specific glycosylation enzymes,change with joint pathology. Therefore, targeting these glycosylationenzymes could result in the development of compounds which may beeffective in diseases where there is extensive matrix degradation. Inaddition, the pattern or levels of these enzymes may also be used asmarkers for disease diagnosis or prognosis. ppGaNTase-T6 is likely tofunction as a specific glycosylation enzyme in cartilage tissue and mayplay a role in pathology of osteoarthritis.

[0020] The biological properties of the ppGaNTase-T6 are hereinafterreferred to as “biological activity of ppGaNTase-T6” or “ppGaNTase-T6activity.” Preferably, a polypeptide of the present invention exhibitsat least one biological activity of ppGaNTase-T6.

[0021] Polypeptides of the present invention also include variants ofthe aforementioned polypeptides, including all allelic forms and splicevariants. Such polypeptides vary from the reference polypeptide byinsertions, deletions, and substitutions that may be conservative ornon-conservative, or any combination thereof. Particularly preferredvariants are those in which several, for instance from 50 to 30, from 30to 20, from 20 to 10, from 10 to 5, from 5 to 3, from 3 to 2, from 2 to1 or 1 amino acids are inserted, substituted, or deleted, in anycombination.

[0022] Preferred fragments of polypeptides of the present inventioninclude an isolated polypeptide comprising an amino acid sequence havingat least 30, 50 or 100 contiguous amino acids from the amino acidsequence of SEQ ID NO: 2, or an isolated polypeptide comprising an aminoacid sequence having at least 30, 50 or 100 contiguous amino acidstruncated or deleted from the amino acid sequence of SEQ ID NO: 2.Preferred fragments are biologically active fragments that mediate thebiological activity of ppGaNTase-T6, including those with a similaractivity or an improved activity, or with a decreased undesirableactivity. Also preferred are those fragments that are antigenic orimmunogenic in an animal, especially in a human.

[0023] Fragments of the polypeptides of the invention may be employedfor producing the corresponding full-length polypeptide by peptidesynthesis; therefore, these variants may be employed as intermediatesfor producing the full-length polypeptides of the invention. Thepolypeptides of the present invention may be in the form of the “mature”protein or may be a part of a larger protein such as a precursor or afusion protein. It is often advantageous to include an additional aminoacid sequence that contains secretory or leader sequences,pro-sequences, sequences that aid in purification, for instance multiplehistidine residues, or an additional sequence for stability duringrecombinant production.

[0024] Polypeptides of the present invention can be prepared in anysuitable manner, for instance by isolation form naturally occurringsources, from genetically engineered host cells comprising expressionsystems (vide infra) or by chemical synthesis, using for instanceautomated peptide synthesizers, or a combination of such methods. Meansfor preparing such polypeptides are well understood in the art.

[0025] In a further aspect, the present invention relates toppGaNTase-T6 polynucleotides. Such polynucleotides include:

[0026] (a) an isolated polynucleotide comprising a polynucleotidesequence having at least 95%, 96%, 97%, 98%, or 99% identity to thepolynucleotide sequence of SEQ ID NO: 1;

[0027] (b) an isolated polynucleotide comprising the polynucleotide ofSEQ ID NO:1;

[0028] (c) an isolated polynucleotide having at least 95%, 96%, 97%,98%, or 99% identity to the polynucleotide of SEQ ID NO:1;

[0029] (d) the isolated polynucleotide of SEQ ID NO:1;

[0030] (e) an isolated polynucleotide comprising a polynucleotidesequence encoding a polypeptide sequence having at least 95%, 96%, 97%,98%, or 99% identity to the polypeptide sequence of SEQ ID NO:2;

[0031] (f) an isolated polynucleotide comprising a polynucleotidesequence encoding the polypeptide of SEQ ID NO:2;

[0032] (g) an isolated polynucleotide having a polynucleotide sequenceencoding a polypeptide sequence having at least 95%, 96%, 97%, 98%, or99% identity to the polypeptide sequence of SEQ ID NO:2;

[0033] (h) an isolated polynucleotide encoding the polypeptide of SEQ IDNO:2;

[0034] (i) an isolated polynucleotide having or comprising apolynucleotide sequence that has an Identity Index of 0.95, 0.96, 0.97,0.98, or 0.99 compared to the polynucleotide sequence of SEQ ID NO: 1;

[0035] (j) an isolated polynucleotide having or comprising apolynucleotide sequence encoding a polypeptide sequence that has anIdentity Index of 0.95, 0.96, 0.97, 0.98, or 0.99 compared to thepolypeptide sequence of SEQ ID NO:2; and polynucleotides that arefragments and variants of the above mentioned polynucleotides or thatare complementary to above mentioned polynucleotides, over the entirelength thereof.

[0036] Preferred fragments of polynucleotides of the present inventioninclude an isolated polynucleotide comprising an nucleotide sequencehaving at least 15, 30, 50 or 100 contiguous nucleotides from thesequence of SEQ ID NO: 1, or an isolated polynucleotide comprising ansequence having at least 30, 50 or 100 contiguous nucleotides truncatedor deleted from the sequence of SEQ ID NO: 1.

[0037] Preferred variants of polynucleotides of the present inventioninclude splice variants, allelic variants, and polymorphisms, includingpolynucleotides having one or more single nucleotide polymorphisms(SNPs).

[0038] Polynucleotides of the present invention also includepolynucleotides encoding polypeptide variants that comprise the aminoacid sequence of SEQ ID NO:2 and in which several, for instance from 50to 30, from 30 to 20, from 20 to 10, from 10 to 5, from 5 to 3, from 3to 2, from 2 to 1 or 1 amino acid residues are substituted, deleted oradded, in any combination.

[0039] In a further aspect, the present invention providespolynucleotides that are RNA transcripts of the DNA sequences of thepresent invention. Accordingly, there is provided an RNA polynucleotidethat:

[0040] (a) comprises an RNA transcript of the DNA sequence encoding thepolypeptide of SEQ ID NO:2;

[0041] (b) is the RNA transcript of the DNA sequence encoding thepolypeptide of SEQ ID NO:2;

[0042] (c) comprises an RNA transcript of the DNA sequence of SEQ IDNO:1; or

[0043] (d) is the RNA transcript of the DNA sequence of SEQ ID NO:1; andRNA polynucleotides that are complementary thereto.

[0044] The polynucleotide sequence of SEQ ID NO:1 shows homology withhuman polynucleotide GalNAc transferase-T4 (ppGaNtase-T4, GenBankAccession # Y08564, Bennet et al. J. Biol. Chem. 273: 30472-30481, 1998)and with rat polynucleotide GalNAc transferase-T1 (ppGaNtase-T5, GenBankAccession # AF049344, Ten Hagen et al. J. Biol. Chem. 273: 27749-27754,1998). The polynucleotide sequence of SEQ ID NO:1 is a cDNA sequencethat encodes the polypeptide of SEQ ID NO:2. The polynucleotide sequenceencoding the polypeptide of SEQ ID NO:2 may be identical to thepolypeptide encoding sequence of SEQ ID NO:1 or it may be a sequenceother than SEQ ID NO:1, which, as a result of the redundancy(degeneracy) of the genetic code, also encodes the polypeptide of SEQ IDNO:2. The polypeptide of SEQ ID NO:2 is related to other proteins of theUDP-GalNac:polypeptide N-acetylgalactosaminyltransferase family, havinghomology and/or structural similarity with human polypeptide GalNActransferase-T4 (ppGaNtase-T4, PID Accession # NP_(—)003765, Bennet etal. J. Biol. Chem. 273: 30472-30481, 1998) and to human polypeptideGalNAc transferase-T3 (ppGaNtase-T3, PID Accession # NP_(—)004473,Bennet et al. J. Biol. Chem. 271: 17006-17012, 1996).

[0045] Preferred polypeptides and polynucleotides of the presentinvention are expected to have, inter alia, similar biologicalfunctions/properties to their homologous polypeptides andpolynucleotides. Furthermore, preferred polypeptides and polynucleotidesof the present invention have at least one ppGaNTase-T6 activity.

[0046] Polynucleotides of the present invention may be obtained usingstandard cloning and screening techniques from a cDNA library derivedfrom mRNA in cells of human osteoarthritic cartilage, (see for instance,Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989)).Polynucleotides of the invention can also be obtained from naturalsources such as genomic DNA libraries or can be synthesized using wellknown and commercially available techniques.

[0047] When polynucleotides of the present invention are used for therecombinant production of polypeptides of the present invention, thepolynucleotide used may include the coding sequence for the maturepolypeptide, by itself, or the coding sequence for the maturepolypeptide in the reading frame with other coding sequences, such asthose encoding a leader or secretory sequence, a pre-, or pro- orprepro-protein sequence, or other fusion peptide portions. For example,a marker sequence that facilitates purification of the fused polypeptidecan be encoded. In certain preferred embodiments of this aspect of theinvention, the marker sequence is a hexa-histidine peptide, as providedin the pQE vector (Qiagen, Inc.) and described in Gentz et al., ProcNatl Acad Sci USA (1989) 86:821-824, or is an HA tag. The polynucleotidemay also contain non-coding 5′ and 3′ sequences, such as transcribed,non-translated sequences, splicing and polyadenylation signals, ribosomebinding sites and sequences that stabilize mRNA.

[0048] Polynucleotides that are identical, or have sufficient identityto a polynucleotide sequence of SEQ ID NO:1, may be used ashybridization probes for cDNA and genomic DNA or as primers for anucleic acid amplification reaction (for instance, PCR). Such probes andprimers may be used to isolate full-length cDNAs and genomic clonesencoding polypeptides of the present invention and to isolate cDNA andgenomic clones of other genes (including genes encoding paralogs fromhuman sources and orthologs and paralogs from species other than human)that have a high sequence similarity to SEQ ID NO:1, typically at least95% identity. Preferred probes and primers will generally comprise atleast 15 nucleotides, preferably, at least 30 nucleotides and may haveat least 50, if not at least 100 nucleotides. Particularly preferredprobes will have between 30 and 50 nucleotides. Particularly preferredprimers will have between 20 and 25 nucleotides.

[0049] A polynucleotide encoding a polypeptide of the present invention,including homologs from species other than human, may be obtained by aprocess comprising the steps of screening a library under stringenthybridization conditions with a labeled probe having the sequence of SEQID NO: 1 or a fragment thereof, preferably of at least 15 nucleotides;and isolating full-length cDNA and genomic clones containing saidpolynucleotide sequence. Such hybridization techniques are well known tothe skilled artisan. Preferred stringent hybridization conditionsinclude overnight incubation at 42° C. in a solution comprising: 50%formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodiumphosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20microgram/ml denatured, sheared salmon sperm DNA; followed by washingthe filters in 0.1×SSC at about 65° C. Thus the present invention alsoincludes isolated polynucleotides, preferably with a nucleotide sequenceof at least 100, obtained by screening a library under stringenthybridization conditions with a labeled probe having the sequence of SEQID NO:1 or a fragment thereof, preferably of at least 15 nucleotides.

[0050] The skilled artisan will appreciate that, in many cases, anisolated cDNA sequence will be incomplete, in that the region coding forthe polypeptide does not extend all the way through to the 5′ terminus.This is a consequence of reverse transcriptase, an enzyme withinherently low “processivity” (a measure of the ability of the enzyme toremain attached to the template during the polymerization reaction),failing to complete a DNA copy of the mRNA template during first strandcDNA synthesis.

[0051] There are several methods available and well known to thoseskilled in the art to obtain full-length cDNAs, or extend short cDNAs,for example those based on the method of Rapid Amplification of cDNAends (RACE) (see, for example, Frohman et al., Proc Nat Acad Sci USA 85,8998-9002, 1988). Recent modifications of the technique, exemplified bythe Marathon (trade mark) technology (Clontech Laboratories Inc.) forexample, have significantly simplified the search for longer cDNAs. Inthe Marathon (trade mark) technology, cDNAs have been prepared from mRNAextracted from a chosen tissue and an ‘adaptor’ sequence ligated ontoeach end. Nucleic acid amplification (PCR) is then carried out toamplify the “missing” 5′ end of the cDNA using a combination of genespecific and adaptor specific oligonucleotide primers. The PCR reactionis then repeated using ‘nested’ primers, that is, primers designed toanneal within the amplified product (typically an adaptor specificprimer that anneals further 3′ in the adaptor sequence and a genespecific primer that anneals further 5′ in the known gene sequence). Theproducts of this reaction can then be analyzed by DNA sequencing and afull-length cDNA constructed either by joining the product directly tothe existing cDNA to give a complete sequence, or carrying out aseparate full-length PCR using the new sequence information for thedesign of the 5′ primer.

[0052] The recombinant polypeptides of the present invention may beprepared by processes well known in the art. In one such example, thepolypeptides are prepared by genetically engineered host cellscomprising expression systems. Accordingly, in a further aspect, thepresent invention relates to expression systems comprising apolynucleotide or polynucleotides of the present invention, to hostcells which are genetically engineered with such expression systems andto the production of polypeptides of the invention by recombinanttechniques. Cell-free translation systems can also be employed toproduce such proteins using RNAs derived from the DNA constructs of thepresent invention.

[0053] For recombinant production, host cells can be geneticallyengineered to incorporate expression systems or portions thereof forpolynucleotides of the present invention. Polynucleotides may beintroduced into host cells by methods described in many standardlaboratory manuals, such as Davis et al., Basic Methods in MolecularBiology (1986) and Sambrook et al. (ibid). Preferred methods ofintroducing polynucleotides into host cells include, for instance,calcium phosphate transfection, DEAE-dextran mediated transfection,transvection, microinjection, cationic lipid-mediated transfection,electroporation, transduction, scrape loading, ballistic introduction orinfection.

[0054] Representative examples of appropriate hosts include bacterialcells, such as Streptococci, Staphylococci, E. coli, Streptomyces andBacillus subtilis cells; fungal cells, such as yeast cells andAspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, HEK 293 andBowes melanoma cells; and plant cells.

[0055] A great variety of expression systems can be used, for instance,chromosomal, episomal and virus-derived systems, e.g., vectors derivedfrom bacterial plasmids, from bacteriophage, from transposons, fromyeast episomes, from insertion elements, from yeast chromosomalelements, from viruses such as baculoviruses, papova viruses, such asSV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabiesviruses and retroviruses, and vectors derived from combinations thereof,such as those derived from plasmid and bacteriophage genetic elements,such as cosmids and phagemids. The expression systems may containcontrol regions that regulate as well as engender expression. Generally,any system or vector that is able to maintain, propagate or express apolynucleotide to produce a polypeptide in a host may be used. Theappropriate polynucleotide sequence may be inserted into an expressionsystem by any of a variety of well-known and routine techniques, suchas, for example, those set forth in Sambrook et al., (ibid). Appropriatesecretion signals may be incorporated into the desired polypeptide toallow secretion of the translated protein into the lumen of theendoplasmic reticulum, the periplasmic space or the extracellularenvironment. These signals may be endogenous to the polypeptide or theymay be heterologous signals.

[0056] If a polypeptide of the present invention is to be expressed foruse in screening assays, it is generally preferred that the polypeptidebe produced at the surface of the cell. In this event, the cells may beharvested prior to use in the screening assay. If the polypeptide issecreted into the medium, the medium can be recovered in order torecover and purify the polypeptide. If produced intracellularly, thecells must first be lysed before the polypeptide is recovered.

[0057] Polypeptides of the present invention can be recovered andpurified from recombinant cell cultures by well-known methods includingammonium sulfate or ethanol precipitation, acid extraction, anion orcation exchange chromatography, phosphocellulose chromatography,hydrophobic interaction chromatography, affinity chromatography,hydroxylapatite chromatography and lectin chromatography. Mostpreferably, high performance liquid chromatography is employed forpurification. Well known techniques for refolding proteins may beemployed to regenerate active conformation when the polypeptide isdenatured during intracellular synthesis, isolation and/or purification.

[0058] Polynucleotides of the present invention may be used asdiagnostic reagents, through detecting mutations in the associated gene.Detection of a mutated form of the gene characterized by thepolynucleotide of SEQ ID NO:1 in the cDNA or genomic sequence and whichis associated with a dysfunction will provide a diagnostic tool that canadd to, or define, a diagnosis of a disease, or susceptibility to adisease, which results from under-expression, over-expression or alteredspatial or temporal expression of the gene. Individuals carryingmutations in the gene may be detected at the DNA level by a variety oftechniques well known in the art.

[0059] Nucleic acids for diagnosis may be obtained from a subject'scells, such as from blood, urine, saliva, tissue biopsy or autopsymaterial. The genomic DNA may be used directly for detection or it maybe amplified enzymatically by using PCR, preferably RT-PCR, or otheramplification techniques prior to analysis. RNA or cDNA may also be usedin similar fashion. Deletions and insertions can be detected by a changein size of the amplified product in comparison to the normal genotype.Point mutations can be identified by hybridizing amplified DNA tolabeled ppGaNTase-T6 nucleotide sequences. Perfectly matched sequencescan be distinguished from mismatched duplexes by RNase digestion or bydifferences in melting temperatures. DNA sequence difference may also bedetected by alterations in the electrophoretic mobility of DNA fragmentsin gels, with or without denaturing agents, or by direct DNA sequencing(see, for instance, Myers et al., Science (1985) 230:1242). Sequencechanges at specific locations may also be revealed by nucleaseprotection assays, such as RNase and S 1 protection or the chemicalcleavage method (see Cotton et al., Proc Natl Acad Sci USA (1985) 85:4397-4401).

[0060] An array of oligonucleotides probes comprising ppGaNTase-T6polynucleotide sequence or fragments thereof can be constructed toconduct efficient screening of e.g., genetic mutations. Such arrays arepreferably high density arrays or grids. Array technology methods arewell known and have general applicability and can be used to address avariety of questions in molecular genetics including gene expression,genetic linkage, and genetic variability, see, for example, M. Chee etal., Science, 274, 610-613 (1996) and other references cited therein.

[0061] Detection of abnormally decreased or increased levels ofpolypeptide or mRNA expression may also be used for diagnosing ordetermining susceptibility of a subject to a disease of the invention.Decreased or increased expression can be measured at the RNA level usingany of the methods well known in the art for the quantification ofpolynucleotides, such as, for example, nucleic acid amplification, forinstance PCR, RT-PCR, RNase protection, Northern blotting and otherhybridization methods. Assay techniques that can be used to determinelevels of a protein, such as a polypeptide of the present invention, ina sample derived from a host are well-known to those of skill in theart. Such assay methods include radioimmunoassays, competitive-bindingassays, Western Blot analysis and ELISA assays.

[0062] Thus in another aspect, the present invention relates to adiagnostic kit comprising:

[0063] (a) a polynucleotide of the present invention, preferably thenucleotide sequence of SEQ ID NO: 1, or a fragment or an RNA transcriptthereof;

[0064] (b) a nucleotide sequence complementary to that of (a);

[0065] (c) a polypeptide of the present invention, preferably thepolypeptide of SEQ ID NO:2 or a fragment thereof; or

[0066] (d) an antibody to a polypeptide of the present invention,preferably to the polypeptide of SEQ ID NO:2.

[0067] It will be appreciated that in any such kit, (a), (b), (c) or (d)may comprise a substantial component. Such a kit will be of use indiagnosing a disease or susceptibility to a disease, particularlydiseases of the invention, amongst others.

[0068] The polynucleotide sequences of the present invention arevaluable for chromosome localization studies. The sequence isspecifically targeted to, and can hybridize with, a particular locationon an individual human chromosome. The mapping of relevant sequences tochromosomes according to the present invention is an important firststep in correlating those sequences with gene associated disease. Once asequence has been mapped to a precise chromosomal location, the physicalposition of the sequence on the chromosome can be correlated withgenetic map data. Such data are found in, for example, V. McKusick,Mendelian Inheritance in Man (available on-line through Johns HopkinsUniversity Welch Medical Library). The relationship between genes anddiseases that have been mapped to the same chromosomal region are thenidentified through linkage analysis (co-inheritance of physicallyadjacent genes). Precise human chromosomal localization for a genomicsequence (gene fragment etc.) can be determined using Radiation Hybrid(RH) Mapping (Walter, M. Spillett, D., Thomas, P., Weissenbach, J., andGoodfellow, P., (1994) A method for constructing radiation hybrid mapsof whole genomes, Nature Genetics 7, 22-28). A number of RH panels areavailable from Research Genetics (Huntsville, Ala., USA) e.g. theGeneBridge4 RH panel (Hum Mol Genet 1996 March;5(3):339-46 A radiationhybrid map of the human genome. Gyapay G, Schmitt K, Fizames C, Jones H,Vega-Czarny N, Spillett D, Muselet D, Prud'Homme J F, Dib C, Auffray C,Morissette J, Weissenbach J, Goodfellow P N). To determine thechromosomal location of a gene using this panel, 93 PCRs are performedusing primers designed from the gene of interest on RH DNAs. Each ofthese DNAs contains random human genomic fragments maintained in ahamster background (human/hamster hybrid cell lines). These PCRs resultin 93 scores indicating the presence or absence of the PCR product ofthe gene of interest. These scores are compared with scores createdusing PCR products from genomic sequences of known location. Thiscomparison is conducted at http://www.genome.wi.mit.edu/.

[0069] The polynucleotide sequences of the present invention are alsovaluable tools for tissue expression studies. Such studies allow thedetermination of expression patterns of polynucleotides of the presentinvention that may give an indication as to the expression patterns ofthe encoded polypeptides in tissues, by detecting the mRNAs that encodethem. The techniques used are well known in the art and include in situhybridization techniques to clones arrayed on a grid, such as cDNAmicroarray hybridization (Schena et al, Science, 270, 467-470, 1995 andShalon et al, Genome Res, 6, 639-645, 1996) and nucleotide amplificationtechniques such as PCR. A preferred method uses the TAQMAN (Trade mark)technology available from Perkin Elmer. Results from these studies canprovide an indication of the normal function of the polypeptide in theorganism. In addition, comparative studies of the normal expressionpattern of mRNAs with that of mRNAs encoded by an alternative form ofthe same gene (for example, one having an alteration in polypeptidecoding potential or a regulatory mutation) can provide valuable insightsinto the role of the polypeptides of the present invention, or that ofinappropriate expression thereof in disease. Such inappropriateexpression may be of a temporal, spatial or simply quantitative nature.

[0070] The polypeptides of the present invention are expressed in normaland osteoarthritic human cartilage.

[0071] A further aspect of the present invention relates to antibodies.The polypeptides of the invention or their fragments, or cellsexpressing them, can be used as immunogens to produce antibodies thatare immunospecific for polypeptides of the present invention. The term“immunospecific” means that the antibodies have substantially greateraffinity for the polypeptides of the invention than their affinity forother related polypeptides in the prior art.

[0072] Antibodies generated against polypeptides of the presentinvention may be obtained by administering the polypeptides orepitope-bearing fragments, or cells to an animal, preferably a non-humananimal, using routine protocols. For preparation of monoclonalantibodies, any technique that provides antibodies produced bycontinuous cell line cultures can be used. Examples include thehybridoma technique (Kohler, G. and Milstein, C., Nature (1975)256:495-497), the trioma technique, the human B-cell hybridoma technique(Kozbor et al., Immunology Today (1983) 4:72) and the EBV-hybridomatechnique (Cole et al., Monoclonal Antibodies and Cancer Therapy, 77-96,Alan R. Liss, Inc., 1985).

[0073] Techniques for the production of single chain antibodies, such asthose described in U.S. Pat. No. 4,946,778, can also be adapted toproduce single chain antibodies to polypeptides of this invention. Also,transgenic mice, or other organisms, including other mammals, may beused to express humanized antibodies.

[0074] The above-described antibodies may be employed to isolate or toidentify clones expressing the polypeptide or to purify the polypeptidesby affinity chromatography. Antibodies against polypeptides of thepresent invention may also be employed to treat diseases of theinvention, amongst others.

[0075] Polypeptides and polynucleotides of the present invention mayalso be used as vaccines. Accordingly, in a further aspect, the presentinvention relates to a method for inducing an immunological response ina mammal that comprises inoculating the mammal with a polypeptide of thepresent invention, adequate to produce antibody and/or T cell immuneresponse, including, for example, cytokine-producing T cells orcytotoxic T cells, to protect said animal from disease, whether thatdisease is already established within the individual or not. Animmunological response in a mammal may also be induced by a methodcomprising delivering a polypeptide of the present invention via avector directing expression of the polynucleotide and coding for thepolypeptide in vivo in order to induce such an immunological response toproduce an antibody to protect said animal from diseases of theinvention. One way of administering the vector is by accelerating itinto the desired cells as a coating on particles or otherwise. Suchnucleic acid vector may comprise DNA, RNA, a modified nucleic acid, or aDNA/RNA hybrid. For use a vaccine, a polypeptide or a nucleic acidvector will be normally provided as a vaccine formulation (composition).The formulation may further comprise a suitable carrier. Since apolypeptide may be broken down in the stomach, it is preferablyadministered parenterally (for instance, subcutaneous, intramuscular,intravenous, or intradermal injection). Formulations suitable forparenteral administration include aqueous and non-aqueous sterileinjection solutions that may contain anti-oxidants, buffers,bacteriostats and solutes that render the formulation isotonic with theblood of the recipient; and aqueous and non-aqueous sterile suspensionsthat may include suspending agents or thickening agents. Theformulations may be presented in unit-dose or multi-dose containers, forexample, sealed ampoules and vials and may be stored in a freeze-driedcondition requiring only the addition of the sterile liquid carrierimmediately prior to use. The vaccine formulation may also includeadjuvant systems for enhancing the immunogenicity of the formulation,such as oil-in water systems and other systems known in the art. Thedosage will depend on the specific activity of the vaccine and can bereadily determined by routine experimentation.

[0076] Polypeptides of the present invention have one or more biologicalfunctions that are of relevance in one or more disease states, inparticular the diseases of the invention mentioned above. It istherefore useful to identify compounds that stimulate or inhibit thefunction or level of the polypeptide. Accordingly, in a further aspect,the present invention provides for a method of screening compounds toidentify those that stimulate or inhibit the function or level of thepolypeptide. Such methods identify agonists or antagonists that may beemployed for therapeutic and prophylactic purposes for such diseases ofthe invention as mentioned herein. Compounds may be identified from avariety of sources, for example, cells, cell-free preparations, chemicallibraries, collections of chemical compounds, and natural productmixtures. Such agonists or antagonists so-identified may be natural ormodified substrates, ligands, receptors, enzymes, etc., as the case maybe, of the polypeptide; a structural or functional mimetic thereof (seeColigan et al., Current Protocols in Immunology 1(2):Chapter 5 (1991))or a small molecule. Such small molecules preferably have a molecularweight below 2,000 daltons, more preferably between 300 and 1,000daltons, and most preferably between 400 and 700 daltons. It ispreferred that these small molecules are organic molecules.

[0077] The screening method may simply measure the binding of acandidate compound to the polypeptide, or to cells or membranes bearingthe polypeptide, or a fusion protein thereof, by means of a labeldirectly or indirectly associated with the candidate compound.Alternatively, the screening method may involve measuring or detecting(qualitatively or quantitatively) the competitive binding of a candidatecompound to the polypeptide against a labeled competitor (e.g. agonistor antagonist). Further, these screening methods may test whether thecandidate compound results in a signal generated by activation orinhibition of the polypeptide, using detection systems appropriate tothe cells bearing the polypeptide. Inhibitors of activation aregenerally assayed in the presence of a known agonist and the effect onactivation by the agonist by the presence of the candidate compound isobserved. Further, the screening methods may simply comprise the stepsof mixing a candidate compound with a solution containing a polypeptideof the present invention, to form a mixture, measuring a ppGaNTase-T6activity in the mixture, and comparing the ppGaNTase-T6 activity of themixture to a control mixture which contains no candidate compound.

[0078] Polypeptides of the present invention may be employed inconventional low capacity screening methods and also in high-throughputscreening (HTS) formats. Such HTS formats include not only thewell-established use of 96- and, more recently, 384-well micotiterplates but also emerging methods such as the nanowell method describedby Schullek et al, Anal Biochem., 246, 20-29, (1997).

[0079] Fusion proteins, such as those made from Fc portion andppGaNTase-T6 polypeptide, as hereinbefore described, can also be usedfor high-throughput screening assays to identify antagonists for thepolypeptide of the present invention (see D. Bennett et al., J MolRecognition, 8:52-58 (1995); and K. Johanson et al., J Biol Chem,270(16):9459-9471 (1995)).

[0080] The polynucleotides, polypeptides and antibodies to thepolypeptide of the present invention may also be used to configurescreening methods for detecting the effect of added compounds on theproduction of mRNA and polypeptide in cells. For example, an ELISA assaymay be constructed for measuring secreted or cell associated levels ofpolypeptide using monoclonal and polyclonal antibodies by standardmethods known in the art. This can be used to discover agents that mayinhibit or enhance the production of polypeptide (also called antagonistor agonist, respectively) from suitably manipulated cells or tissues.

[0081] A polypeptide of the present invention may be used to identifymembrane bound or soluble receptors, if any, through standard receptorbinding techniques known in the art. These include, but are not limitedto, ligand binding and crosslinking assays in which the polypeptide islabeled with a radioactive isotope (for instance, ¹²⁵I), chemicallymodified (for instance, biotinylated), or fused to a peptide sequencesuitable for detection or purification, and incubated with a source ofthe putative receptor (cells, cell membranes, cell supernatants, tissueextracts, bodily fluids). Other methods include biophysical techniquessuch as surface plasmon resonance and spectroscopy. These screeningmethods may also be used to identify agonists and antagonists of thepolypeptide that compete with the binding of the polypeptide to itsreceptors, if any. Standard methods for conducting such assays are wellunderstood in the art.

[0082] Examples of antagonists of polypeptides of the present inventioninclude antibodies or, in some cases, oligonucleotides or proteins thatare closely related to the ligands, substrates, receptors, enzymes,etc., as the case may be, of the polypeptide, e.g., a fragment of theligands, substrates, receptors, enzymes, etc.; or a small molecule thatbind to the polypeptide of the present invention but do not elicit aresponse, so that the activity of the polypeptide is prevented.

[0083] Screening methods may also involve the use of transgenictechnology and ppGaNTase-T6 gene. The art of constructing transgenicanimals is well established. For example, the ppGaNTase-T6 gene may beintroduced through microinjection into the male pronucleus of fertilizedoocytes, retroviral transfer into pre- or post-implantation embryos, orinjection of genetically modified, such as by electroporation, embryonicstem cells into host blastocysts. Particularly useful transgenic animalsare so-called “knock-in” animals in which an animal gene is replaced bythe human equivalent within the genome of that animal. Knock-intransgenic animals are useful in the drug discovery process, for targetvalidation, where the compound is specific for the human target. Otheruseful transgenic animals are so-called “knock-out” animals in which theexpression of the animal ortholog of a polypeptide of the presentinvention and encoded by an endogenous DNA sequence in a cell ispartially or completely annulled. The gene knock-out may be targeted tospecific cells or tissues, may occur only in certain cells or tissues asa consequence of the limitations of the technology, or may occur in all,or substantially all, cells in the animal. Transgenic animal technologyalso offers a whole animal expression-cloning system in which introducedgenes are expressed to give large amounts of polypeptides of the presentinvention.

[0084] Screening kits for use in the above described methods form afurther aspect of the present invention. Such screening kits comprise:

[0085] (a) a polypeptide of the present invention;

[0086] (b) a recombinant cell expressing a polypeptide of the presentinvention;

[0087] (c) a cell membrane expressing a polypeptide of the presentinvention; or

[0088] (d) an antibody to a polypeptide of the present invention;

[0089] which polypeptide is preferably that of SEQ ID NO:2.

[0090] It will be appreciated that in any such kit, (a), (b), (c) or (d)may comprise a substantial component.

[0091] GLOSSARY

[0092] The following definitions are provided to facilitateunderstanding of certain terms used frequently hereinbefore.

[0093] “Antibodies” as used herein includes polyclonal and monoclonalantibodies, chimeric, single chain, and humanized antibodies, as well asFab fragments, including the products of an Fab or other immunoglobulinexpression library.

[0094] “Isolated” means altered “by the hand of man” from its naturalstate, i.e., if it occurs in nature, it has been changed or removed fromits original environment, or both. For example, a polynucleotide or apolypeptide naturally present in a living organism is not “isolated,”but the same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated”, as the term is employedherein. Moreover, a polynucleotide or polypeptide that is introducedinto an organism by transformation, genetic manipulation or by any otherrecombinant method is “isolated” even if it is still present in saidorganism, which organism may be living or non-living.

[0095] “Polynucleotide” generally refers to any polyribonucleotide (RNA)or polydeoxribonucleotide (DNA), which may be unmodified or modified RNAor DNA. “Polynucleotides” include, without limitation, single- anddouble-stranded DNA, DNA that is a mixture of single- anddouble-stranded regions, single- and double-stranded RNA, and RNA thatis mixture of single- and double-stranded regions, hybrid moleculescomprising DNA and RNA that may be single-stranded or, more typically,double-stranded or a mixture of single- and double-stranded regions. Inaddition, “polynucleotide” refers to triple-stranded regions comprisingRNA or DNA or both RNA and DNA. The term “polynucleotide” also includesDNAs or RNAs containing one or more modified bases and DNAs or RNAs withbackbones modified for stability or for other reasons. “Modified” basesinclude, for example, tritylated bases and unusual bases such asinosine. A variety of modifications may be made to DNA and RNA; thus,“polynucleotide” embraces chemically, enzymatically or metabolicallymodified forms of polynucleotides as typically found in nature, as wellas the chemical forms of DNA and RNA characteristic of viruses andcells. “Polynucleotide” also embraces relatively short polynucleotides,often referred to as oligonucleotides.

[0096] “Polypeptide” refers to any polypeptide comprising two or moreamino acids joined to each other by peptide bonds or modified peptidebonds, i.e., peptide isosteres. “Polypeptide” refers to both shortchains, commonly referred to as peptides, oligopeptides or oligomers,and to longer chains, generally referred to as proteins. Polypeptidesmay contain amino acids other than the 20 gene-encoded amino acids.“Polypeptides” include amino acid sequences modified either by naturalprocesses, such as post-translational processing, or by chemicalmodification techniques that are well known in the art. Suchmodifications are well-described in basic texts and in more detailedmonographs, as well as in a voluminous research literature.Modifications may occur anywhere in a polypeptide, including the peptidebackbone, the amino acid side-chains and the amino or carboxyl termini.It will be appreciated that the same type of modification may be presentto the same or varying degrees at several sites in a given polypeptide.Also, a given polypeptide may contain many types of modifications.Polypeptides may be branched as a result of ubiquitination, and they maybe cyclic, with or without branching. Cyclic, branched and branchedcyclic polypeptides may result from post-translation natural processesor may be made by synthetic methods. Modifications include acetylation,acylation, ADP-ribosylation, amidation, biotinylation, covalentattachment of flavin, covalent attachment of a heme moiety, covalentattachment of a nucleotide or nucleotide derivative, covalent attachmentof a lipid or lipid derivative, covalent attachment ofphosphotidylinositol, cross-linking, cyclization, disulfide bondformation, demethylation, formation of covalent cross-links, formationof cystine, formation of pyroglutamate, formylation,gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation,iodination, methylation, myristoylation, oxidation, proteolyticprocessing, phosphorylation, prenylation, racemization, selenoylation,sulfation, transfer-RNA mediated addition of amino acids to proteinssuch as arginylation, and ubiquitination (see, for instance,Proteins—Structure and Molecular Properties, 2nd Ed., T. E. Creighton,W. H. Freeman and Company, New York, 1993; Wold, F., Post-translationalProtein Modifications: Perspectives and Prospects, 1-12, inPost-translational Covalent Modification of Proteins, B. C. Johnson,Ed., Academic Press, New York, 1983; Seifter et al., “Analysis forprotein modifications and nonprotein cofactors”, Meth Enzymol, 182,626-646, 1990, and Rattan et al., “Protein Synthesis: Post-translationalModifications and Aging”, Ann NY Acad Sci, 663, 48-62, 1992).

[0097] “Fragment” of a polypeptide sequence refers to a polypeptidesequence that is shorter than the reference sequence but that retainsessentially the same biological function or activity as the referencepolypeptide. “Fragment” of a polynucleotide sequence refers to apolynucleotide sequence that is shorter than the reference sequence ofSEQ ID NO:1.

[0098] “Variant” refers to a polynucleotide or polypeptide that differsfrom a reference polynucleotide or polypeptide, but retains theessential properties thereof. A typical variant of a polynucleotidediffers in nucleotide sequence from the reference polynucleotide.Changes in the nucleotide sequence of the variant may or may not alterthe amino acid sequence of a polypeptide encoded by the referencepolynucleotide. Nucleotide changes may result in amino acidsubstitutions, additions, deletions, fusions and truncations in thepolypeptide encoded by the reference sequence, as discussed below. Atypical variant of a polypeptide differs in amino acid sequence from thereference polypeptide. Generally, alterations are limited so that thesequences of the reference polypeptide and the variant are closelysimilar overall and, in many regions, identical. A variant and referencepolypeptide may differ in amino acid sequence by one or moresubstitutions, insertions, deletions in any combination. A substitutedor inserted amino acid residue may or may not be one encoded by thegenetic code. Typical conservative substitutions include Gly, Ala; Val,Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe and Tyr. Avariant of a polynucleotide or polypeptide may be naturally occurringsuch as an allele, or it may be a variant that is not known to occurnaturally. Non-naturally occurring variants of polynucleotides andpolypeptides may be made by mutagenesis techniques or by directsynthesis. Also included as variants are polypeptides having one or morepost-translational modifications, for instance glycosylation,phosphorylation, methylation, ADP ribosylation and the like. Embodimentsinclude methylation of the N-terminal amino acid, phosphorylations ofserines and threonines and modification of C-terminal glycines.

[0099] “Allele” refers to one of two or more alternative forms of a geneoccurring at a given locus in the genome.

[0100] “Polymorphism” refers to a variation in nucleotide sequence (andencoded polypeptide sequence, if relevant) at a given position in thegenome within a population.

[0101] “Single Nucleotide Polymorphism” (SNP) refers to the occurrenceof nucleotide variability at a single nucleotide position in the genome,within a population. An SNP may occur within a gene or within intergenicregions of the genome. SNPs can be assayed using Allele SpecificAmplification (ASA). For the process at least 3 primers are required. Acommon primer is used in reverse complement to the polymorphism beingassayed. This common primer can be between 50 and 1500 bps from thepolymorphic base. The other two (or more) primers are identical to eachother except that the final 3′ base wobbles to match one of the two (ormore) alleles that make up the polymorphism. Two (or more) PCR reactionsare then conducted on sample DNA, each using the common primer and oneof the Allele Specific Primers.

[0102] “Splice Variant” as used herein refers to cDNA molecules producedfrom RNA molecules initially transcribed from the same genomic DNAsequence but which have undergone alternative RNA splicing. AlternativeRNA splicing occurs when a primary RNA transcript undergoes splicing,generally for the removal of introns, which results in the production ofmore than one mRNA molecule each of that may encode different amino acidsequences. The term splice variant also refers to the proteins encodedby the above cDNA molecules.

[0103] “Identity” reflects a relationship between two or morepolypeptide sequences or two or more polynucleotide sequences,determined by comparing the sequences. In general, identity refers to anexact nucleotide to nucleotide or amino acid to amino acidcorrespondence of the two polynucleotide or two polypeptide sequences,respectively, over the length of the sequences being compared.

[0104] “% Identity”—For sequences where there is not an exactcorrespondence, a “% identity” may be determined. In general, the twosequences to be compared are aligned to give a maximum correlationbetween the sequences. This may include inserting “gaps” in either oneor both sequences, to enhance the degree of alignment. A % identity maybe determined over the whole length of each of the sequences beingcompared (so-called global alignment), that is particularly suitable forsequences of the same or very similar length, or over shorter, definedlengths (so-called local alignment), that is more suitable for sequencesof unequal length.

[0105] “Similarity” is a further, more sophisticated measure of therelationship between two polypeptide sequences. In general, “similarity”means a comparison between the amino acids of two polypeptide chains, ona residue by residue basis, taking into account not only exactcorrespondences between a between pairs of residues, one from each ofthe sequences being compared (as for identity) but also, where there isnot an exact correspondence, whether, on an evolutionary basis, oneresidue is a likely substitute for the other. This likelihood has anassociated “score” from which the “% similarity” of the two sequencescan then be determined.

[0106] Methods for comparing the identity and similarity of two or moresequences are well known in the art. Thus for instance, programsavailable in the Wisconsin Sequence Analysis Package, version 9.1(Devereux J et al, Nucleic Acids Res, 12, 387-395, 1984, available fromGenetics Computer Group, Madison, Wis., USA), for example the programsBESTFIT and GAP, may be used to determine the % identity between twopolynucleotides and the % identity and the % similarity between twopolypeptide sequences. BESTFIT uses the “local homology” algorithm ofSmith and Waterman (J Mol Biol, 147,195-197, 1981, Advances in AppliedMathematics, 2, 482-489, 1981) and finds the best single region ofsimilarity between two sequences. BESTFIT is more suited to comparingtwo polynucleotide or two polypeptide sequences that are dissimilar inlength, the program assuming that the shorter sequence represents aportion of the longer. In comparison, GAP aligns two sequences, findinga “maximum similarity”, according to the algorithm of Neddleman andWunsch (J Mol Biol, 48, 443-453, 1970). GAP is more suited to comparingsequences that are approximately the same length and an alignment isexpected over the entire length. Preferably, the parameters “Gap Weight”and “Length Weight” used in each program are 50 and 3, forpolynucleotide sequences and 12 and 4 for polypeptide sequences,respectively. Preferably, % identities and similarities are determinedwhen the two sequences being compared are optimally aligned.

[0107] Other programs for determining identity and/or similarity betweensequences are also known in the art, for instance the BLAST family ofprograms (Altschul S F et al, J Mol Biol, 215, 403-410, 1990, Altschul SF et al, Nucleic Acids Res., 25:389-3402, 1997, available from theNational Center for Biotechnology Information (NCBI), Bethesda, Md., USAand accessible through the home page of the NCBI atwww.ncbi.nlm.nih.gov) and FASTA (Pearson W R, Methods in Enzymology,183, 63-99, 1990; Pearson W R and Lipman D J, Proc Nat Acad Sci USA, 85,2444-2448,1988, available as part of the Wisconsin Sequence AnalysisPackage).

[0108] Preferably, the BLOSUM62 amino acid substitution matrix (HenikoffS and Henikoff J G, Proc. Nat. Acad Sci. USA, 89, 10915-10919, 1992) isused in polypeptide sequence comparisons including where nucleotidesequences are first translated into amino acid sequences beforecomparison.

[0109] Preferably, the program BESTFIT is used to determine the %identity of a query polynucleotide or a polypeptide sequence withrespect to a reference polynucleotide or a polypeptide sequence, thequery and the reference sequence being optimally aligned and theparameters of the program set at the default value, as hereinbeforedescribed.

[0110] “Identity Index” is a measure of sequence relatedness that may beused to compare a candidate sequence (polynucleotide or polypeptide) anda reference sequence. Thus, for instance, a candidate polynucleotidesequence having, for example, an Identity Index of 0.95 compared to areference polynucleotide sequence is identical to the reference sequenceexcept that the candidate polynucleotide sequence may include on averageup to five differences per each 100 nucleotides of the referencesequence. Such differences are selected from the group consisting of atleast one nucleotide deletion, substitution, including transition andtransversion, or insertion. These differences may occur at the 5′ or 3′terminal positions of the reference polynucleotide sequence or anywherebetween these terminal positions, interspersed either individually amongthe nucleotides in the reference sequence or in one or more contiguousgroups within the reference sequence. In other words, to obtain apolynucleotide sequence having an Identity Index of 0.95 compared to areference polynucleotide sequence, an average of up to 5 in every 100 ofthe nucleotides of the in the reference sequence may be deleted,substituted or inserted, or any combination thereof, as hereinbeforedescribed. The same applies mutatis mutandis for other values of theIdentity Index, for instance 0.96, 0.97, 0.98 and 0.99.

[0111] Similarly, for a polypeptide, a candidate polypeptide sequencehaving, for example, an Identity Index of 0.95 compared to a referencepolypeptide sequence is identical to the reference sequence except thatthe polypeptide sequence may include an average of up to fivedifferences per each 100 amino acids of the reference sequence. Suchdifferences are selected from the group consisting of at least one aminoacid deletion, substitution, including conservative and non-conservativesubstitution, or insertion. These differences may occur at the amino- orcarboxy-terminal positions of the reference polypeptide sequence oranywhere between these terminal positions, interspersed eitherindividually among the amino acids in the reference sequence or in oneor more contiguous groups within the reference sequence. In other words,to obtain a polypeptide sequence having an Identity Index of 0.95compared to a reference polypeptide sequence, an average of up to 5 inevery 100 of the amino acids in the reference sequence may be deleted,substituted or inserted, or any combination thereof, as hereinbeforedescribed. The same applies mutatis mutandis for other values of theIdentity Index, for instance 0.96, 0.97, 0.98 and 0.99.

[0112] The relationship between the number of nucleotide or amino aciddifferences and the Identity Index may be expressed in the followingequation:

n _(a) ≦x _(a)(x _(a) ·I)

[0113] in which:

[0114] n_(a) is the number of nucleotide or amino acid differences,

[0115] x_(a) is the total number of nucleotides or amino acids in SEQ IDNO:1 or SEQ ID NO:2, respectively,

[0116] I is the Identity Index,

[0117] · is the symbol for the multiplication operator, and

[0118] in which any non-integer product of x_(a) and I is rounded downto the nearest integer prior to subtracting it from x_(a).

[0119] “Homolog” is a generic term used in the art to indicate apolynucleotide or polypeptide sequence possessing a high degree ofsequence relatedness to a reference sequence. Such relatedness may bequantified by determining the degree of identity and/or similaritybetween the two sequences as hereinbefore defined. Falling within thisgeneric term are the terms “ortholog”, and “paralog”. “Ortholog” refersto a polynucleotide or polypeptide that is the functional equivalent ofthe polynucleotide or polypeptide in another species. “Paralog” refersto a polynucleotide or polypeptide that within the same species which isfunctionally similar.

[0120] “Fusion protein” refers to a protein encoded by two, oftenunrelated, fused genes or fragments thereof. In one example, EP-A-0 464533-A discloses fusion proteins comprising various portions of constantregion of imrmunoglobulin molecules together with another human proteinor part thereof. In many cases, employing an immunoglobulin Fc region asa part of a fusion protein is advantageous for use in therapy anddiagnosis resulting in, for example, improved pharmacokinetic properties[see, e.g., EP-A 0232 262]. On the other hand, for some uses it would bedesirable to be able to delete the Fc part after the fusion protein hasbeen expressed, detected and purified.

[0121] All publications and references, including but not limited topatents and patent applications, cited in this specification are hereinincorporated by reference in their entirety as if each individualpublication or reference were specifically and individually indicated tobe incorporated by reference herein as being fully set forth. Any patentapplication to which this application claims priority is alsoincorporated by reference herein in its entirety in the manner describedabove for publications and references.

EXAMPLE 1 Cloning of ppGaNTase-T6 full Length cDNA

[0122] An assembly containing 9 ESTs from human osteoarthritic cartilagecDNA library was chosen for analysis as it represented a completelyunknown gene. One of the ESTs, HOA12F10, from this assembly was fullysequenced. The full length sequence contained 3357 nucleotides with asingle open reading frame of 1917 nucleotides encoding a polypeptide of639 amino acids. The predicted protein appears to be a novel homologueof UDP-GalNac:polypeptide N-acetylgalactosaminyltransferases (ppGaNTase,EC 2.4.1.41) family of sugar transferring enzyme and hence it was termedppGaNTase-T6. Sequence analysis suggests that ppGaNTase-T6 contains anN-terminal 13-amino acid (aa) cytoplasmic tail, followed by a 20-aahydrophobic sequence (as predicted by the algorithm of von Heijne, Eur.J. Bioch. 133:17-21, 1983), followed by a 125-aa stem region and a 481aa catalytic domain that has extensive homology to various ppGaNTases.Like other members of this family, ppGaNTase-T6 is likely to be a typeII transmembrane protein with its catalytic domain in Golgi apparatusand N-terminus tail in the cytoplasm.

[0123] A database search revealed several ESTs with homology to variousregions of ppGaNTase-T6. The majority of these ESTs come from humanosteoarthritic cartilage suggesting that the ppGaNTase-T6 is highlyexpressed in this tissue. Few ESTs were also identified from a publicGenBank database search. These ESTs were from placenta, fetal heart,testes and libraries of mixed tissues (melanocyte, pregnant uterus andfetal heart; lung, testes and B-cells).

EXAMPLE 2 Tissue Distribution

[0124] Two multiple tissue Northern blots (prepared using 24 humantissues and cell lines) were screened using a ppGaNTase-T6 cDNA probeusing a standard procedure (Sambrook et al., Molecular Cloning: alaboratory manual, 2nd Ed. Cold Spring Harbor Lab Press, NY (1989). Theexpression of a single ˜4.5 Kb mRNA was detected only in the normal andosteoarthritic cartilage and osteosarcoma Saos2 cells.

1 2 1 1920 DNA HOMO SAPIENS 1 atgctcctaa ggaagcgata caggcacagaccatgcagac tccagttcct cctgctgctc 60 ctgatgctgg gatgcgtcct gatgatggtggcgatgttgc accctcccca ccacaccctg 120 caccagactg tcacagccca agccagcaagcacagccctg aagccaggta ccgcctggac 180 tttggggaat cccaggattg ggtactggaagctgaggatg agggtgaaga gtacagccct 240 ctggagggcc tgccaccctt tatctcactgcgggaggatc agctgctggt ggccgtggcc 300 ttaccccagg ccagaaggaa ccagagccagggcaggagag gtgggagcta ccgcctcatc 360 aagcagccaa ggaggcagga taaggaagccccaaagaggg actggggggc tgatgaggac 420 ggggaggtgt ctgaagaaga ggagttgaccccgttcagcc tggacccacg tggcctccag 480 gaggcactca gtgcccgcat ccccctccagagggctctgc ccgaggtgcg gcacccactg 540 tgtctgcagc agcaccctca ggacagcctgcccacagcca gcgtcatcct ctgtttccat 600 gatgaggcct ggtccactct cctgcggactgtacacagca tcctcgacac agtgcccagg 660 gccttcctga aggagatcat cctcgtggacgacctcagcc agcaaggaca actcaagtct 720 gctctcagcg aatatgtggc caggctggagggggtgaagt tactcaggag caacaagagg 780 ctgggtgcca tcagggcccg gatgctgggggccaccagag ccaccgggga tgtgctcgtc 840 ttcatggatg cccactgcga gtgccacccaggctggctgg agcccctcct cagcagaata 900 gctggtgaca ggagccgagt ggtatctccggtgatagatg tgattgactg gaagactttc 960 cagtattacc cctcaaagga cctgcagcgtggggtgttgg actggaagct ggatttccac 1020 tgggaacctt tgccagagca tgtgaggaaggccctccagt cccccataag ccccatcagg 1080 agccctgtgg tgcccggaga ggtggtggccatggacagac attacttcca aaacactgga 1140 gcgtatgact ctcttatgtc gctgcgaggtggtgaaaacc tcgaactgtc tttcaaggcc 1200 tggctctgtg gtggctctgt tgaaatccttccctgctctc gggtaggaca catctaccaa 1260 aatcaggatt cccattcccc cctcgaccaggaggccaccc tgaggaacag ggttcgcatt 1320 gctgagacct ggctggggtc attcaaagaaaccttctaca agcatagccc agaggccttc 1380 tccttgagca aggctgagaa gccagactgcatggaacgct tgcagctgca aaggagactg 1440 ggttgtcgga cattccactg gtttctggctaatgtctacc ctgagctgta cccatctgaa 1500 cccaggccca gtttctctgg aaagctccacaacactggac ttgggctctg tgcagactgc 1560 caggcagaag gggacatcct gggctgtcccatggtgttgg ctccttgcag tgacagccgg 1620 cagcaacagt acctgcagca caccagcaggaaggagattc actttggcag cccacagcac 1680 ctgtgctttg ctgtcaggca ggagcaggtgattcttcaga actgcacgga ggaaggcctg 1740 gccatccacc agcagcactg ggacttccaggagaatggga tgattgtcca cattctttct 1800 gggaaatgca tggaagctgt ggtgcaagaaaacaataaag atttgtacct gcgtccgtgt 1860 gatggaaaag cccgccagca gtggcgttttgaccagatca atgctgtgga tgaacgatga 1920 2 639 PRT HOMO SAPIENS 2 Met LeuLeu Arg Lys Arg Tyr Arg His Arg Pro Cys Arg Leu Gln Phe 1 5 10 15 LeuLeu Leu Leu Leu Met Leu Gly Cys Val Leu Met Met Val Ala Met 20 25 30 LeuHis Pro Pro His His Thr Leu His Gln Thr Val Thr Ala Gln Ala 35 40 45 SerLys His Ser Pro Glu Ala Arg Tyr Arg Leu Asp Phe Gly Glu Ser 50 55 60 GlnAsp Trp Val Leu Glu Ala Glu Asp Glu Gly Glu Glu Tyr Ser Pro 65 70 75 80Leu Glu Gly Leu Pro Pro Phe Ile Ser Leu Arg Glu Asp Gln Leu Leu 85 90 95Val Ala Val Ala Leu Pro Gln Ala Arg Arg Asn Gln Ser Gln Gly Arg 100 105110 Arg Gly Gly Ser Tyr Arg Leu Ile Lys Gln Pro Arg Arg Gln Asp Lys 115120 125 Glu Ala Pro Lys Arg Asp Trp Gly Ala Asp Glu Asp Gly Glu Val Ser130 135 140 Glu Glu Glu Glu Leu Thr Pro Phe Ser Leu Asp Pro Arg Gly LeuGln 145 150 155 160 Glu Ala Leu Ser Ala Arg Ile Pro Leu Gln Arg Ala LeuPro Glu Val 165 170 175 Arg His Pro Leu Cys Leu Gln Gln His Pro Gln AspSer Leu Pro Thr 180 185 190 Ala Ser Val Ile Leu Cys Phe His Asp Glu AlaTrp Ser Thr Leu Leu 195 200 205 Arg Thr Val His Ser Ile Leu Asp Thr ValPro Arg Ala Phe Leu Lys 210 215 220 Glu Ile Ile Leu Val Asp Asp Leu SerGln Gln Gly Gln Leu Lys Ser 225 230 235 240 Ala Leu Ser Glu Tyr Val AlaArg Leu Glu Gly Val Lys Leu Leu Arg 245 250 255 Ser Asn Lys Arg Leu GlyAla Ile Arg Ala Arg Met Leu Gly Ala Thr 260 265 270 Arg Ala Thr Gly AspVal Leu Val Phe Met Asp Ala His Cys Glu Cys 275 280 285 His Pro Gly TrpLeu Glu Pro Leu Leu Ser Arg Ile Ala Gly Asp Arg 290 295 300 Ser Arg ValVal Ser Pro Val Ile Asp Val Ile Asp Trp Lys Thr Phe 305 310 315 320 GlnTyr Tyr Pro Ser Lys Asp Leu Gln Arg Gly Val Leu Asp Trp Lys 325 330 335Leu Asp Phe His Trp Glu Pro Leu Pro Glu His Val Arg Lys Ala Leu 340 345350 Gln Ser Pro Ile Ser Pro Ile Arg Ser Pro Val Val Pro Gly Glu Val 355360 365 Val Ala Met Asp Arg His Tyr Phe Gln Asn Thr Gly Ala Tyr Asp Ser370 375 380 Leu Met Ser Leu Arg Gly Gly Glu Asn Leu Glu Leu Ser Phe LysAla 385 390 395 400 Trp Leu Cys Gly Gly Ser Val Glu Ile Leu Pro Cys SerArg Val Gly 405 410 415 His Ile Tyr Gln Asn Gln Asp Ser His Ser Pro LeuAsp Gln Glu Ala 420 425 430 Thr Leu Arg Asn Arg Val Arg Ile Ala Glu ThrTrp Leu Gly Ser Phe 435 440 445 Lys Glu Thr Phe Tyr Lys His Ser Pro GluAla Phe Ser Leu Ser Lys 450 455 460 Ala Glu Lys Pro Asp Cys Met Glu ArgLeu Gln Leu Gln Arg Arg Leu 465 470 475 480 Gly Cys Arg Thr Phe His TrpPhe Leu Ala Asn Val Tyr Pro Glu Leu 485 490 495 Tyr Pro Ser Glu Pro ArgPro Ser Phe Ser Gly Lys Leu His Asn Thr 500 505 510 Gly Leu Gly Leu CysAla Asp Cys Gln Ala Glu Gly Asp Ile Leu Gly 515 520 525 Cys Pro Met ValLeu Ala Pro Cys Ser Asp Ser Arg Gln Gln Gln Tyr 530 535 540 Leu Gln HisThr Ser Arg Lys Glu Ile His Phe Gly Ser Pro Gln His 545 550 555 560 LeuCys Phe Ala Val Arg Gln Glu Gln Val Ile Leu Gln Asn Cys Thr 565 570 575Glu Glu Gly Leu Ala Ile His Gln Gln His Trp Asp Phe Gln Glu Asn 580 585590 Gly Met Ile Val His Ile Leu Ser Gly Lys Cys Met Glu Ala Val Val 595600 605 Gln Glu Asn Asn Lys Asp Leu Tyr Leu Arg Pro Cys Asp Gly Lys Ala610 615 620 Arg Gln Gln Trp Arg Phe Asp Gln Ile Asn Ala Val Asp Glu Arg625 630 635

What is claimed is:
 1. An isolated polypeptide selected from the groupconsisting of: (a) an isolated polypeptide encoded by a polynucleotidecomprising the sequence of SEQ ID NO:1; (b) an isolated polypeptidecomprising a polypeptide sequence having at least 95% identity to thepolypeptide sequence of SEQ ID NO:2; (c) an isolated polypeptidecomprising the polypeptide sequence of SEQ ID NO:2; (d) an isolatedpolypeptide having at least 95% identity to the polypeptide sequence ofSEQ ID NO:2; (e) the polypeptide sequence of SEQ ID NO:2; and (f)fragments and variants of such polypeptides in (a) to (e).
 2. Anisolated polynucleotide selected from the group consisting of: (a) anisolated polynucleotide comprising a polynucleotide sequence having atleast 95% identity to the polynucleotide sequence of SEQ ID NO:1; (b) anisolated polynucleotide comprising the polynucleotide of SEQ ID NO:1;(c) an isolated polynucleotide having at least 95% identity to thepolynucleotide of SEQ ID NO:1; (d) the isolated polynucleotide of SEQ IDNO:1; (e) an isolated polynucleotide comprising a polynucleotidesequence encoding a polypeptide sequence having at least 95% identity tothe polypeptide sequence of SEQ ID NO:2; (f) an isolated polynucleotidecomprising a polynucleotide sequence encoding the polypeptide of SEQ IDNO:2; (g) an isolated polynucleotide having a polynucleotide sequenceencoding a polypeptide sequence having at least 95% identity to thepolypeptide sequence of SEQ ID NO:2; (h) an isolated polynucleotideencoding the polypeptide of SEQ ID NO:2; (i) an isolated polynucleotidewith a nucleotide sequence of at least 100 nucleotides obtained byscreening a library under stringent hybridization conditions with alabeled probe having the sequence of SEQ ID NO: 1 or a fragment thereofhaving at least 15 nucleotides; and (j) a polynucleotide which is theRNA equivalent of a polynucleotide of (a) to (i); or a polynucleotidesequence complementary to said isolated polynucleotide andpolynucleotides that are variants and fragments of the above mentionedpolynucleotides or that are complementary to above mentionedpolynucleotides, over the entire length thereof.
 3. An antibodyimmunospecific for the polypeptide of claim
 1. 4. The antibody asclaimed in claim 3 which is a polyclonal antibody.
 5. An expressionvector comprising a polynucleotide capable of producing the polypeptideof claim 1 when said expression vector is present in a compatible hostcell.
 6. A process for producing a recombinant host cell which comprisesthe step of introducing an expression vector comprising a polynucleotidecapable of producing a polypeptide of claim 1 into a cell such that thehost cell, under appropriate culture conditions, produces saidpolypeptide.
 7. A recombinant host cell produced by the process of claim6.
 8. A membrane of the recombinant host cell of claim 7 expressing saidpolypeptide.
 9. A process for producing a polypeptide which comprisesculturing the host cell of claim 7 under conditions sufficient for theproduction of said polypeptide and recovering said polypeptide from theculture.